Hi,<br><br>Thanks for the fast feedback.<br><br>Below the commands that do the job. I am not yet happy with the image quality<br>compared to our normal reconstruction, but it is a start. Any suggestions how to improve<br>continue?<br><br>C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e<br>xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml --proj_iso_x=-21.63 --p<br>roj_iso_y=-54.08<br><br>C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g geometry<br>1.xml -p water -r .*.tif -o water.mha --spacing=0.169 --dimension=256,640,256<br><br>Kind regards,<br>Erik Maddox.<br><br><blockquote style="margin-right: 0px; margin-left:15px;">----Original Message----<br>From : Cyril.Mory@philips.com<br>Date : 26/08/2013 13:39<br>To : simon.rit@creatis.insa-lyon.fr<br>Cc : emaddox@planet.nl, rtk-users@openrtk.org<br>Subject : RE: [Rtk-users] how can I get a good 3d image?<br><br>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Oups. My bad, I didn’t know that.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" lang="EN-US">Thanks for your correction.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D" lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">De :</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> simon.rit@gmail.com [mailto:simon.rit@gmail.com]
<b>De la part de</b> Simon Rit<br>
<b>Envoyé :</b> lundi 26 août 2013 13:33<br>
<b>À :</b> MORY, CYRIL<br>
<b>Cc :</b> emaddox@planet.nl; rtk-users@openrtk.org<br>
<b>Objet :</b> Re: [Rtk-users] how can I get a good 3d image?<o:p></o:p></span></p>
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<p class="MsoNormal">Hi,<o:p></o:p></p>
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<p class="MsoNormal">Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see<br>
<a href="http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html">http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html</a><o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">It assumes that the maximum possible value is I0. You can check the result with<br>
rtkprojections -p. -r .*.tif -o proj.mha<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the
projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point.<br>
Simon<o:p></o:p></p>
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<p class="MsoNormal">On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL <<a href="mailto:Cyril.Mory@philips.com" target="_blank">Cyril.Mory@philips.com</a>> wrote:<o:p></o:p></p>
<p class="MsoNormal">Hi Erik,<br>
<br>
Judging from the projection image you sent, you seem to be missing a crucial step.<br>
<br>
The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each<br>
pixel of the detector. Before you backproject this, you have to convert it to attenuations.<br>
<br>
Check out the Wikipedia page <a href="http://en.wikipedia.org/wiki/Tomographic_reconstruction" target="_blank">
http://en.wikipedia.org/wiki/Tomographic_reconstruction</a>.<br>
Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction.<br>
<br>
Best regards,<br>
Cyril<br>
<br>
-----Message d'origine-----<br>
De : <a href="mailto:rtk-users-bounces@openrtk.org">rtk-users-bounces@openrtk.org</a> [mailto:<a href="mailto:rtk-users-bounces@openrtk.org">rtk-users-bounces@openrtk.org</a>] De la part de
<a href="mailto:emaddox@planet.nl">emaddox@planet.nl</a><br>
Envoyé : lundi 26 août 2013 11:48<br>
À : <a href="mailto:rtk-users@openrtk.org">rtk-users@openrtk.org</a><br>
Objet : [Rtk-users] how can I get a good 3d image?<o:p></o:p></p>
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Hi,<br>
<br>
I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success.<br>
I carefully checked all hints on the website and looked to the examples which I could run on my system.<br>
<br>
My data is acquired in a cone beam CT system.<br>
<br>
My projections are tif images, 103 images each rotated by 1.98 degree steps.<br>
The images are 640 by 512 pixels.<br>
<br>
Distances: source to detector is 255 mm, source to centre object is 200 mm<br>
<br>
commands I used:<br>
<br>
rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml<br>
<br>
rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169<br>
<br>
(I tried --dimension with single slice and all slices (640))<br>
<br>
my projections:<br>
<br>
<a href="http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8" target="_blank">http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8</a> (30 Mb)<br>
<br>
can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom?<br>
<br>
Kind regards,<br>
Erik Maddox.<br>
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